PDB-9bjl: Crystal structure of Influenza D virus Nucleoprotein (Oklahoma)

ID or keywords:

Entry

Database: PDB / ID: 9bjl

Title

Crystal structure of Influenza D virus Nucleoprotein (Oklahoma)

Components

Nucleoprotein

Keywords

VIRAL PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / INFLUENZA VIRUS / NUCLEOPROTEIN / Influenzavirus D Influenza D virus D/bovine

Function / homology

Function and homology information

helical viral capsid / viral penetration into host nucleus / viral nucleocapsid / ribonucleoprotein complex / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function

Biological species

Influenza D virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.43 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of Influenza D virus Nucleoprotein (Oklahoma)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Apr 25, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9bjl.cif.gz	720 KB	Display	PDBx/mmCIF format
PDB format	pdb9bjl.ent.gz	594.5 KB	Display	PDB format
PDBx/mmJSON format	9bjl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9bjl_validation.pdf.gz	469.2 KB	Display	wwPDB validaton report
Full document	9bjl_full_validation.pdf.gz	483.2 KB	Display
Data in XML	9bjl_validation.xml.gz	58.1 KB	Display
Data in CIF	9bjl_validation.cif.gz	80.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bj/9bjl ftp://data.pdbj.org/pub/pdb/validation_reports/bj/9bjl	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Nucleoprotein

B: Nucleoprotein

C: Nucleoprotein

D: Nucleoprotein

hetero molecules

254 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	74.461, 84.501, 88.728
Angle α, β, γ (deg.)	102.34, 97.37, 97.14
Int Tables number	1
Space group name H-M	P1

#1: Protein	Nucleoprotein Mass: 63408.461 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza D virus / Gene: NP / Plasmid: InvdC.18714.a.PQ11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: W5RBB9
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.6 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 2.4M Malonate, pH 4.0, InvdC.18714.a.PQ11.PS38729 at 40 mg/mL. plate Liu-S-115 C2, Puck: PSL-0806, Cryo: 3.4M Malonate, pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 13, 2024
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.43→85.57 Å / Num. obs: 71662 / % possible obs: 91.9 % / Redundancy: 2.4 % / CC_1/2: 0.997 / R_merge(I) obs: 0.075 / R_pim(I) all: 0.058 / R_rim(I) all: 0.095 / Χ²: 0.99 / Net I/σ(I): 8.2 / Num. measured all: 169069
Reflection shell	Resolution: 2.43→2.49 Å / % possible obs: 97.1 % / Redundancy: 2.4 % / R_merge(I) obs: 0.63 / Num. measured all: 13744 / Num. unique obs: 5626 / CC_1/2: 0.591 / R_pim(I) all: 0.489 / R_rim(I) all: 0.802 / Χ²: 0.96 / Net I/σ(I) obs: 1.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.21_5207: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.43→85.57 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.241	3510	4.9 %
R_work	0.2032	-	-
obs	0.2051	71645	91.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.43→85.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14412	0	1	43	14456

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	14653
X-RAY DIFFRACTION	f_angle_d	0.761	19680
X-RAY DIFFRACTION	f_dihedral_angle_d	12.507	5551
X-RAY DIFFRACTION	f_chiral_restr	0.044	2173
X-RAY DIFFRACTION	f_plane_restr	0.012	2533

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.43-2.46	0.3397	145	0.3027	2922	X-RAY DIFFRACTION	97
2.46-2.5	0.325	133	0.2804	2860	X-RAY DIFFRACTION	97
2.5-2.54	0.3154	149	0.271	2888	X-RAY DIFFRACTION	97
2.54-2.58	0.3463	167	0.2673	2915	X-RAY DIFFRACTION	98
2.58-2.62	0.323	141	0.262	2852	X-RAY DIFFRACTION	97
2.62-2.66	0.2981	140	0.2549	2513	X-RAY DIFFRACTION	89
2.68-2.71	0.276	107	0.2564	2016	X-RAY DIFFRACTION	95
2.71-2.76	0.3133	140	0.257	2899	X-RAY DIFFRACTION	97
2.76-2.82	0.2895	174	0.2571	2807	X-RAY DIFFRACTION	97
2.82-2.88	0.3174	144	0.2515	2876	X-RAY DIFFRACTION	97
2.88-2.95	0.3238	133	0.2443	2878	X-RAY DIFFRACTION	97
2.95-3.02	0.2777	149	0.2358	2884	X-RAY DIFFRACTION	97
3.02-3.1	0.3014	143	0.2408	2885	X-RAY DIFFRACTION	97
3.1-3.19	0.2992	137	0.2276	2868	X-RAY DIFFRACTION	97
3.19-3.3	0.2724	146	0.2159	2871	X-RAY DIFFRACTION	97
3.3-3.41	0.2701	129	0.2219	2761	X-RAY DIFFRACTION	93
3.42-3.55	0.2668	87	0.2166	1998	X-RAY DIFFRACTION	68
3.55-3.71	0.2372	118	0.1983	2190	X-RAY DIFFRACTION	73
3.71-3.91	0.1972	140	0.1721	2328	X-RAY DIFFRACTION	80
3.91-4.15	0.1756	143	0.161	2779	X-RAY DIFFRACTION	93
4.16-4.48	0.1974	163	0.1573	2770	X-RAY DIFFRACTION	94
4.48-4.93	0.1823	138	0.151	2836	X-RAY DIFFRACTION	95
4.93-5.64	0.2322	128	0.1819	2851	X-RAY DIFFRACTION	96
5.64-7.1	0.2391	157	0.2005	2834	X-RAY DIFFRACTION	96
7.1-85.57	0.1864	159	0.1794	2854	X-RAY DIFFRACTION	96

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.1167	-0.53	-0.5274	0.3863	0.6109	0.7992	0.0625	0.0947	-0.0159	-0.1067	-0.0761	0.038	-0.345	0.039	-0.0018	0.3739	-0.0616	-0.0225	0.3657	0.0586	0.3042	0.8917	42.4328	-34.0429
2	0.6073	0.0087	-0.6635	-0.0261	0.0847	0.6713	0.0928	0.0258	0.0697	0.3597	0.0282	-0.065	-0.0884	0.2013	-0	0.4804	-0.0274	-0.0106	0.3563	0.0354	0.4044	-3.392	31.9037	-14.0701
3	0.2982	0.4493	-0.5384	0.1229	0.3643	0.9084	0.0519	0.1339	0.01	0.1142	-0.0551	-0.0379	-0.1291	-0.106	0	0.4836	0.0028	-0.0134	0.382	0.0676	0.3679	-8.4581	26.5507	-16.4271
4	0.4638	-0.1514	-0.223	0.9035	-0.3892	0.4533	-0.0013	0.0067	-0.1519	-0.1717	0.0782	-0.1674	0.0095	0.003	-0	0.2912	-0.0366	0.0288	0.3994	0.0073	0.3641	10.6805	25.2643	-32.4249
5	-0.3082	0.439	-0.0816	0.9697	-0.1614	0.3047	0.0019	-0.1036	-0.1651	0.0704	-0.1216	-0.1595	-0.0246	0.0744	-0.0003	0.3738	-0.0034	0.0017	0.48	0.028	0.4392	-1.1117	11.7013	-18.3433
6	0.3066	-0.0406	-0.0594	0.0549	-0.1163	0.2452	-0.3241	-0.2587	-0.3308	-0.3813	-0.0745	-0.0931	-0.0092	0.639	-0.078	0.4506	0.0059	-0.1274	0.6441	0.0748	0.568	16.6968	18.9567	-15.609
7	0.8187	0.2297	0.5353	0.6432	0.8027	0.8477	0.1373	0.1853	-0.3229	0.0254	-0.1135	0.1317	0.3733	0.0154	-0	0.6608	-0.1284	-0.1727	0.6239	-0.09	0.5501	-41.9377	-22.4754	-29.9063
8	0.7987	0.1131	0.9389	1.7875	0.4151	2.0824	0.1157	0.1031	-0.1509	-0.0968	-0.0081	0.1814	0.1761	-0.1321	0.0316	0.3294	-0.0081	-0.0014	0.4071	-0.0298	0.371	-31.3098	-8.7382	-11.8804
9	0.7609	0.8056	1.2384	-0.2681	-0.3117	1.4462	0.3307	0.5177	-0.6453	0.001	0.4237	-0.1927	0.6024	0.8108	1.4855	0.587	0.1762	-0.0831	0.5727	-0.2804	0.403	-19.7638	-21.3857	-24.1737
10	1.1305	0.8045	2.1655	-0.5897	-0.2301	0.8616	0.2239	0.3309	-0.3287	-0.035	-0.0128	0.0117	0.1713	0.5495	0.3827	0.4382	0.0939	-0.004	0.4377	-0.0415	0.4152	-10.8207	-11.5746	-3.6933
11	1.3072	-0.7629	-0.8007	0.5144	0.1968	0.6888	-0.1173	-0.2026	0.0896	0.0878	0.0049	0.1443	-0.0791	0.1448	0	0.4363	-0.0144	0.0189	0.4208	0.0431	0.4142	-2.6272	-42.0048	37.6608
12	1.2073	0.0466	-0.1428	1.1761	0.1409	0.2152	0.0681	-0.0222	0.0575	0.047	-0.0452	0.1079	-0.1014	0.2143	0	0.3628	0.0064	0.0178	0.355	-0.0125	0.3405	-11.1598	-19.6295	28.9618
13	0.2697	0.0969	0.3852	0.7567	-0.42	0.7464	-0.0278	-0.1164	0.1284	0.1966	0.0298	-0.0762	-0.1341	-0.1148	-0	0.4091	-0.0032	0.01	0.3284	0.0027	0.3459	-5.6433	-16.9823	26.717
14	0.5465	-0.1182	-0.0061	1.9772	-0.4555	0.8198	-0.0073	-0.0442	0.0092	-0.0787	-0.0698	-0.3052	0.0578	0.1854	-0	0.3416	0.0398	0.0262	0.2751	0.0022	0.3959	4.9293	-35.3	19.9301
15	0.5182	0.703	-0.3733	0.3829	-1.0572	0.2872	0.2969	0.1165	-0.219	-0.0586	-0.1708	0.021	-0.0396	-0.0285	0	0.3886	0.0183	-0.0071	0.3245	-0.0298	0.4447	3.3584	2.9422	16.9608
16	0.281	-0.5671	0.4923	0.3543	-0.2999	0.3265	0.1549	0.2625	-0.0479	-0.2574	-0.128	-0.3404	0.0257	0.098	-0	0.4581	0.0385	0.0857	0.4479	-0.0041	0.4783	7.5273	-20.7663	11.8954
17	0.7893	0.1656	-0.2098	1.0998	0.2902	0.376	0.0802	-0.2304	0.3396	-0.0055	-0.0179	-0.2727	0.0044	0.2394	0	0.407	-0.0353	0.0009	0.4676	-0.048	0.513	39.1086	26.1588	32.605
18	1.1923	-0.0633	-0.0331	0.0711	-0.2021	0.2882	0.1302	-0.109	0.118	-0.0521	-0.0348	-0.0443	-0.0602	0.0475	-0	0.3304	0.0161	0.051	0.3107	-0.0273	0.3427	16.2686	21.8714	23.3427
19	1.3256	0.2919	0.2119	0.8767	-0.1879	1.0216	0.0425	0.0034	-0.0503	0.0314	0.0806	-0.1744	0.1075	0.1954	0	0.3408	0.061	0.0445	0.3993	-0.0179	0.3867	35.9216	11.57	18.2003
20	0.2832	-0.0279	0.0265	0.1139	-0.1928	0.1316	-0.1727	-0.0696	-0.2334	0.1275	0.1924	-0.2955	-0.2104	0.5154	-0	0.4523	0.0388	-0.0346	0.5007	0.0923	0.4598	8.3588	16.5779	-9.2144
21	0.2185	0.3418	0.0409	0.3412	0.3077	0.7314	-0.0036	0.2314	-0.0077	-0.6722	-0.305	0.494	-0.3127	0.0166	-0.0226	0.4896	-0.011	0.0163	0.3913	0.0405	0.4109	-1.2636	15.8852	7.6428
22	0.8758	0.6283	-0.4078	0.2274	-0.2885	0.066	-0.0269	0.4541	-0.3953	-0.1617	0.07	0.0757	0.1407	-0.2076	-0.0063	0.4962	0.1186	-0.0158	0.4431	-0.0862	0.49	26.0087	7.3999	7.9281

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 143 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 144 through 194 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 195 through 288 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 289 through 358 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 359 through 489 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 490 through 514 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 8 through 115 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 116 through 288 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 289 through 420 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 421 through 509 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 8 through 123 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 124 through 233 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 234 through 288 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 289 through 401 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 402 through 464 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 465 through 511 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 8 through 115 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 116 through 288 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 289 through 401 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 402 through 430 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 431 through 469 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 470 through 511 )

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